This function is written with chromosome maps in mind but generalized for visualizing much more. All that is required is a data frame of segmants with columns called band, start, end.
band: Which band does the segmant belong to (y-axis)start : Start location of index (x-axis)end : End location of index (x-axis)In the future, I plan to keep it as generalized as possible, maximizing its flexibility and application in various types of analyses. Feel free to suggest ideas, report bugs, or contribute!
source("bands.R")chromosomes <- c(paste("chr", 1:21, sep=""), "chrX", "chrY", "chrM")
df <- read.table('data/df.txt', sep="\t", header=TRUE, stringsAsFactors=FALSE)df.1 <- df[sample(1:nrow(df), 2500, replace=F),]
head(df.1) band start end name
16058 chr8 86048372 86069697 RNU6ATAC41P
24774 chr12 56237806 56244727 MIR196A2
33304 chr19 813583 813653 LINC00683
34660 chr19 49255471 49256102 NLRP2
21664 chr10 125700435 125719460 EDRF1-AS1
18868 chrX 77885376 77885634 DRP2draw.bands(df.1, chromosomes, labels=F)df.2 <- df.1
df.2$color <- ifelse(sample(c(T, T, T, F), 2500, replace=T), "grey", "firebrick")
head(df.2) band start end name color
16058 chr8 86048372 86069697 RNU6ATAC41P grey
24774 chr12 56237806 56244727 MIR196A2 grey
33304 chr19 813583 813653 LINC00683 firebrick
34660 chr19 49255471 49256102 NLRP2 firebrick
21664 chr10 125700435 125719460 EDRF1-AS1 grey
18868 chrX 77885376 77885634 DRP2 firebrickdraw.bands(df.2, chromosomes, labels=F)df.3 <- head(df.2, 500)
head(df.3) band start end name color
16058 chr8 86048372 86069697 RNU6ATAC41P grey
24774 chr12 56237806 56244727 MIR196A2 grey
33304 chr19 813583 813653 LINC00683 firebrick
34660 chr19 49255471 49256102 NLRP2 firebrick
21664 chr10 125700435 125719460 EDRF1-AS1 grey
18868 chrX 77885376 77885634 DRP2 firebrickdraw.bands(df.3, chromosomes, labels=T)